Provided by: libbio-perl-perl_1.7.2-3_all bug

NAME

       Bio::SearchIO::Writer::TextResultWriter - Object to implement writing a
       Bio::Search::ResultI in Text.

SYNOPSIS

         use Bio::SearchIO;
         use Bio::SearchIO::Writer::TextResultWriter;

         my $in = Bio::SearchIO->new(-format => 'blast',
                                    -file   => shift @ARGV);

         my $writer = Bio::SearchIO::Writer::TextResultWriter->new();
         my $out = Bio::SearchIO->new(-writer => $writer);
         $out->write_result($in->next_result);

DESCRIPTION

       This object implements the SearchWriterI interface which will produce a set of Text for a
       specific Bio::Search::Report::ReportI interface.

       You can also provide the argument -filters => \%hash to filter the at the hsp, hit, or
       result level.  %hash is an associative array which contains any or all of the keys (HSP,
       HIT, RESULT).  The values pointed to by these keys would be references to a subroutine
       which expects to be passed an object - one of Bio::Search::HSP::HSPI,
       Bio::Search::Hit::HitI, and Bio::Search::Result::ResultI respectively.  Each function
       needs to return a boolean value as to whether or not the passed element should be included
       in the output report - true if it is to be included, false if it to be omitted.

       For example to filter on sequences in the database which are too short for your criteria
       you would do the following.

       Define a hit filter method

         sub hit_filter {
             my $hit = shift;
             return $hit->length E<gt> 100; # test if length of the hit sequence
                                            # long enough
         }
         my $writer = Bio::SearchIO::Writer::TextResultWriter->new(
              -filters => { 'HIT' =E<gt> \&hit_filter }
             );

       Another example would be to filter HSPs on percent identity, let's only include HSPs which
       are 75% identical or better.

          sub hsp_filter {
              my $hsp = shift;
              return $hsp->percent_identity E<gt> 75;
          }
          my $writer = Bio::SearchIO::Writer::TextResultWriter->new(
              -filters => { 'HSP' =E<gt> \&hsp_filter }
             );

       See Bio::SearchIO::SearchWriterI for more info on the filter method.

       This module will use the module Text::Wrap if it is installed to wrap the Query
       description line.  If you do not have Text::Wrap installed this module will work fine but
       you won't have the Query line wrapped.  You will see a warning about this when you first
       instantiate a TextResultWriter - to avoid these warnings from showing up, simply set the
       verbosity upon initialization to -1 like this: my $writer = new
       Bio::SearchIO::Writer::TextResultWriter(-verbose => -1);

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send
       your comments and suggestions preferably to the Bioperl mailing list.  Your participation
       is much appreciated.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their
       resolution. Bug reports can be submitted via the web:

         https://github.com/bioperl/bioperl-live/issues

AUTHOR - Jason Stajich

       Email jason@bioperl.org

APPENDIX

       The rest of the documentation details each of the object methods.  Internal methods are
       usually preceded with a _

   new
        Title   : new
        Usage   : my $obj = Bio::SearchIO::Writer::TextResultWriter->new();
        Function: Builds a new Bio::SearchIO::Writer::TextResultWriter object
        Returns : Bio::SearchIO::Writer::TextResultWriter
        Args    : -filters => hashref with any or all of the keys (HSP HIT RESULT)
                  which have values pointing to a subroutine reference
                  which will expect to get a Hit,HSP, Result object respectively
                  -no_wublastlinks => boolean. Do not display WU-BLAST lines even if
                                      they are parsed out
                                      Links = (1)

   to_string
        Purpose   : Produces data for each Search::Result::ResultI in a string.
                  : This is an abstract method. For some useful implementations,
                  : see ResultTableWriter.pm, HitTableWriter.pm,
                  : and HSPTableWriter.pm.
        Usage     : print $writer->to_string( $result_obj, @args );
        Argument  : $result_obj = A Bio::Search::Result::ResultI object
                  : @args = any additional arguments used by your implementation.
        Returns   : String containing data for each search Result or any of its
                  : sub-objects (Hits and HSPs).
        Throws    : n/a

   start_report
         Title   : start_report
         Usage   : $index->start_report( CODE )
         Function: Stores or returns the code to
                   write the start of the <HTML> block, the <TITLE> block
                   and the start of the <BODY> block of HTML.   Useful
                   for (for instance) specifying alternative
                   HTML if you are embedding the output in
                   an HTML page which you have already started.
                   (For example a routine returning a null string).
                   Returns \&default_start_report (see below) if not
                   set.
         Example : $index->start_report( \&my_start_report )
         Returns : ref to CODE if called without arguments
         Args    : CODE

   default_start_report
        Title   : default_start_report
        Usage   : $self->default_start_report($result)
        Function: The default method to call when starting a report.
        Returns : sting
        Args    : First argument is a Bio::Search::Result::ResultI

   title
        Title   : title
        Usage   : $self->title($CODE)

         Function: Stores or returns the code to provide HTML for the given
                   BLAST report that will appear at the top of the BLAST report
                   HTML output.  Useful for (for instance) specifying
                   alternative routines to write your own titles.
                   Returns \&default_title (see below) if not
                   set.
         Example : $index->title( \&my_title )
         Returns : ref to CODE if called without arguments
         Args    : CODE

   default_title
        Title   : default_title
        Usage   : $self->default_title($result)
        Function: Provides HTML for the given BLAST report that will appear
                  at the top of the BLAST report output.
        Returns : empty for text implementation
        Args    : First argument is a Bio::Search::Result::ResultI

   introduction
        Title   : introduction
        Usage   : $self->introduction($CODE)

         Function: Stores or returns the code to provide HTML for the given
                   BLAST report detailing the query and the
                   database information.
                   Useful for (for instance) specifying
                   routines returning alternative introductions.
                   Returns \&default_introduction (see below) if not
                   set.
         Example : $index->introduction( \&my_introduction )
         Returns : ref to CODE if called without arguments
         Args    : CODE

   default_introduction
        Title   : default_introduction
        Usage   : $self->default_introduction($result)
        Function: Outputs HTML to provide the query
                  and the database information
        Returns : string containing HTML
        Args    : First argument is a Bio::Search::Result::ResultI
                  Second argument is string holding literature citation

   end_report
        Title   : end_report
        Usage   : $self->end_report()
        Function: The method to call when ending a report, this is
                  mostly for cleanup for formats which require you to
                  have something at the end of the document (</BODY></HTML>)
                  for HTML
        Returns : string
        Args    : none

   id_parser
         Title   : id_parser
         Usage   : $index->id_parser( CODE )
         Function: Stores or returns the code used by record_id to
                   parse the ID for record from a string.  Useful
                   for (for instance) specifying a different
                   parser for different flavours of FASTA file.
                   Returns \&default_id_parser (see below) if not
                   set. If you supply your own id_parser
                   subroutine, then it should expect a fasta
                   description line.  An entry will be added to
                   the index for each string in the list returned.
         Example : $index->id_parser( \&my_id_parser )
         Returns : ref to CODE if called without arguments
         Args    : CODE

   default_id_parser
         Title   : default_id_parser
         Usage   : $id = default_id_parser( $header )
         Function: The default Fasta ID parser for Fasta.pm
                   Returns $1 from applying the regexp /^>\s*(\S+)/
                   to $header.
         Returns : ID string
         Args    : a fasta header line string

   algorithm_reference
        Title   : algorithm_reference
        Usage   : my $reference = $writer->algorithm_reference($result);
        Function: Returns the appropriate Bibliographic reference for the
                  algorithm format being produced
        Returns : String
        Args    : L<Bio::Search::Result::ResultI> to reference

   Methods Bio::SearchIO::SearchWriterI
       Bio::SearchIO::SearchWriterI inherited methods.

   filter
        Title   : filter
        Usage   : $writer->filter('hsp', \&hsp_filter);
        Function: Filter out either at HSP,Hit,or Result level
        Returns : none
        Args    : string => data type,
                  CODE reference

   no_wublastlinks
        Title   : no_wublastlinks
        Usage   : $obj->no_wublastlinks($newval)
        Function: Get/Set boolean value regarding whether or not to display
                  Link = (1)
                  type output in the report output (WU-BLAST only)
        Returns : boolean
        Args    : on set, new boolean value (a scalar or undef, optional)

perl v5.28.0                                2018-10-2Bio::SearchIO::Writer::TextResultWriter(3pm)